Manhattan: A bank robbery. Two mutants dressed as X-Men are forcing the director of the bank, Mr. Philbert, to open the vault, but he says that the vault can't be opened until 10 AM. One the mutants doesn't like this answer so he tears apart the vault with his bare hands instead.
As he is occupied with the vault, a guards of the bank takes advantage of the situation and fires his gun at the two mutants, but the bullets bounce off the skin of the first mutant and the second mutant's invisible force field.
Meanwhile the cops arrive at the bank having received the burglar alarm. They try to stop the two mutants, but the cops are no match for them though. They can’t reach the mutant with the forcefield and the other one tosses the cops around. The “X-Men“ get away safely in Mr. Philbert's limousine.
In Xavier's school Cyclops is packing his bags and secretly leaves the mansion. He is still considering himself a menace to the people he cares about because of his power and hopes to find a doctor that will remove his deadly eye beams so that he can be together with Jean.
At the same time the other X-Men are watching the news on TV and learn about the bank robbery in their name. They immediately rush to the professor, but Xavier is already ahead of them. He was following the newscast mentally and has already started to work on the new Cerebro. This improved version can not only detect mutants, it can also show images of them on a screen. Xavier activates the machine and two faint images appear on the screen, the X-Men recognize them as the Blob and Unus, the Untouchable.
The professor suspects that Unus and the Blob aren't operating on their own and tries to use his power to detect the person behind the robbery but somehow that third foe has shielded himself off with a mental screen.
The X-Men prepare to move out but realize that Cyclops is not present and searching for him they find a short note in which Scott says goodbye to them.
Elsewhere Lucifer is gloating as the Blob and Unus unknowingly helped him. Lucifer has build an 'Ultra Scanner' that can locate mutants like Cerebro. When he used it he found the Blob and Unus as opponents in a wrestling match and curiously observed. Soon the two wrestlers discovered they were both mutants and unable to defeat each other, as the Blob could not reach Unus through his forcefield and Unus could not harm the immovable Blob. The match ended in a draw and they two villains later met in the Blob’s trailer.
They talked about each other‘s experiences with the X-Men and decided to work together and commit several crimes, while framing the X-Men for it. However they are unaware that it was Lucifer who planted these ideas into their heads.
In his civilian clothes, Cyclops is wandering around the city when he sees Unus and the Blob in the middle of their second crime. They are once again dressed as X-Men and are robbing a money truck. Although Scott would prefer not to interfere since he left the X-Men, he is afraid that all mutants will be condemned for this crime so he changes into his costume and confronts the villains. Cyclops calls them imposters, but Unus and the Blob keep pretending that they are all X-Men so eventually the nearby crowd turns against Cyclops and he is forced to get out. He decides to return to the X-Men so they can defeat the Blob and Unus as a team.
Meanwhile, Lucifer watches on a monitor and is angry that only one X-Man showed up and he wants full revenge on them. Yet, he then observes the Angel, Beast and Iceman moving towards the Blob and Unus. The two evil mutants are carrying away a money bag as the X-Men arrive and Beast immediately tries to use the Ray Gun, which has defeated Unus before, but somehow Unus appears to be immune against the Ray Gun. Neither the X-Men nor Unus himself know that Lucifer made Unus immune against the device.
When the X-Men attack Unus and the Blob they are confronted with a new danger; the crowd still thinks they are evil mutants so they attack the X-Men as well. While an old woman hits Beast with an umbrella, a police offer is trying to shoot Angel, but he manages to dodge the bullets. The crowd scatters when Blob and Unus run towards the Beast but then Cyclops returns and blasts a hole right in front of the two villains. They fall through the hole right on top of a subway-train, which carries them away.
In his hidden lab somewhere in the great desert of the United States, Lucifer notices that Professor Xavier is trying to locate him. He himself was unable to locate the X-Men's hideout, but now that the professor has made contact with him, he shoots a blast of energy into the atmosphere that rides on the mental waves straight towards the professor.
At the mansion, Xavier has just learned Lucifer's identity when the blast hits him, putting him into a sort of coma. Marvel Girl, who was with the professor at the time he was hit, checks his vital signs and then places a mental-wave amplifier on her head so she can contact the professor mentally. The professor explains to Jean that it was Lucifer who attacked him. In order for the X-Men to defeat him they need to know the full history of their enmity and so Xavier starts telling her about his first encounter with Lucifer.
A few years, back in the days the professor could still walk, Xavier is driving a jeep in Tibet and approaches a walled city. He has heard strange tales about this city and intends to investigate those rumors. As he approaches the gate he is stopped by some guards and the professor immediately feels that the guards are under the mental influence of a powerful being. He also senses strange machines inside the citadel where this being resides. He mentally examines the machines and discovers that they are made of a strange alloy which isn't found on earth, so the being must be from another world. He deducts that the machine keeps some selected people in the city under his control so he convinces the people to start a rebellion against their "ruler".
The professor explains his plans to the people in one of the houses, but then one of them is still under the alien’s mental control and cuts a rope of a chandelier. The professor's mutant brain was able to detect the falling chandelier and he dodges it in time. The traitor is apprehended and this is a clear sign that the alien is aware of the people's upcoming rebellion, so the professor decides to act now. As the people rush towards the citadel they are caught in a tunnel, whose walls are closing in, crushing the people.
However, the professor's powers locate the machinery that operates the walls and he quickly pulls the plug from it. As soon as the walls stop moving they are confronted with the next danger - a fireball shooting straight through the tunnel. But once again the professor saves the locals by opening a hatch which engulfs the people with water which extinguishes the fireball.
The people spread throughout the citadel and take it over completely, yet the alien is still free. In another section of the base, the alien gets a call from “the supreme one“ who orders him to relocate to a new base. As the alien tries to get away he stumbles upon the professor who was looking for him. The alien introduces himself as “Lucifer“ and he pushes a switch which causes a large concrete block to fall right on top of the professor. As Lucifer leaves by stepping through a wall Xavier is left behind with crushed legs.
The professor tells Jean that the incident with Lucifer which costs him his legs was one of many reasons to start the X-Men. He knew that one day he would have to face Lucifer and his alien race again.
Meanwhile Lucifer comes to the conclusion that his devices work properly. Back then in Asia he controlled an entire city, and now with the Blob and Unus he has also mastered to control humans from long distances. He calls his leader, the “Supreme One“, and tells that the time for takeover has come. The Supreme One joyfully announces the coming of Dominus.
Meanwhile the X-Men have returned to their school and Jean fills them in on the professor’s condition and his revelations regarding Lucifer. Still paralyzed, the professor gives Jean mental instructions to have Beast build a "beam distorter" which will allow him to break the paralysis. Fortunately it works and the X-Men start loading a private jet, which the professor had recently purchased. Minutes later the team takes off and set course towards the southwestern desert to face Lucifer.